DELLY v1.1.3 vs v1.2.6

[Faizal-Eeman]

A brief comparison between DELLY v1.1.3 and v1.2.6 prior to pipeline updates.

A germline sample commonly used to test call-gSV was used for the comparison and with GRCh38 as the reference.
Sample path: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/input/data/CPCG0196-B1-downsampled-a-partial-sorted.bam

Germline SV calling:

All significant SVs are shared between v1.1.3 and v1.2.6.
A few SVs appear to be uniquely called by v1.1.3 and not called by v1.2.6, but these SVs can generally be ignored because of the following reasons.

• MAPQ of supporting reads is zero
• variant filter is LowQual
• Paired End (PE) or Split Read (SR) support is very low
• Either one or both breakpoints overlap with soft-masked regions in GRCh38

Comparison files:
unique to v1.1.3 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gSV/DELLY-1.1.3-only.txt
unique to v1.2.6 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gSV/DELLY-1.2.6-only.txt
common SVs - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gSV/intersect-DELLY-1.1.3-DELLY-1.2.6.txt

Germline CNV calling:

All significant CNVs are shared between v1.1.3 and v1.2.6.
One unique CNV is called each v1.1.3 and v1.2.6 but based on the Read-depth based Copy Number estimate (RDCN), this unique variant appears to be a false call.

Comparison files:
unique to v1.1.3 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gCNV/DELLY-1.1.3-only.txt
unique to v1.2.6 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gCNV/DELLY-1.2.6-only.txt
common SVs - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/gCNV/intersect-DELLY-1.1.3-DELLY-1.2.6.txt

Conclusion

All variants are shared between the two versions. A few variants are uniquely called by v1.1.3 but they are likely false positive or low quality variants that can be safely ignored. This suggests improvements in v1.2.6 and therefore, DELLY can be upgraded to v1.2.6 in pipeline-call-gSV.

[Faizal-Eeman]

Somatic SV calling:

A-mini Tumor/Normal pair was used for testing.
Tumor: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/input/data/TWGSAMIN000001-T003-S03-F.bam
Normal: /hot/software/pipeline/pipeline-call-sSV/Nextflow/development/input/data/TWGSAMIN000001-N003-S03-F.bam

All significant SVs are shared between v1.1.3 and v1.2.6.
A few SVs appear to be uniquely called by v1.1.3 and not called by v1.2.6, but these SVs can generally be ignored because of the following reasons.

• MAPQ of supporting reads is zero
• Either one or both breakpoints overlap with soft-masked regions in GRCh38
• Either one or both breakpoints overlap with intergenic regions

Comparison files:
unique to v1.1.3 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/sSV/DELLY-1.1.3-only.txt
unique to v1.2.6 - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/sSV/DELLY-1.2.6-only.txt
common SVs - /hot/software/image/docker-Delly/Docker/development/1.2.6/DELLY-1.1.3-vs-DELLY-1.2.6/sSV/intersect-DELLY-1.1.3-vs-DELLY-1.2.6.txt

Conclusion

DELLY can be upgraded to v1.2.6 in pipeline-call-sSV.